Part I, Part II, Part III
In Chapter four, titled "God the Magician," Miller takes as his main interlocutor Berkeley Law Professor Phillip Johnson who wrote the book Darwin on Trial. Johnson, building on his trade as a lawyer, attempts to create in his reader a "shadow of a doubt" as to the veracity of the science of evolution. In order to create this "shadow of a doubt," Johnson exploits a mid-20th century intra-scientific debate that took place among community of evolutionary biologist: namely, the debate between punctuated equilibrium and phyletic gradualism.
Though the two sides of this debate use the highly technical terms "phyletic gradualism" and "punctuated equilibrium," the concepts are actually quite simple. Phyletic gradualism is essentially the original Darwinian idea that species would develop gradually over millions of years. In this case the fossil record should demonstrate a number of gradual changes in form as species develop. Yet, this, apparently is not what the fossil record shows. Enter Stephen J. Gould, Niles Eldredge, and punctuated equilibrium. Gould and Eldredge, both evolutionary biologists, shook up the scientific community in the 1970s with their theory of punctuated equilibrium. By closely examining the fossil record, Gould and Eldredge argued that what the fossils actually show is a punctuated speciation event in a geological instant followed by long geological periods of stability among species. Just like that, Gould and Eldredge had overturned over a century of scientific wisdom about the evolution of life on planet earth.
Phillip Johnson jumped on this apparent instability in the scientific community regarding evolution and used it to write his book to cast doubt on the theory of evolution. He noted that punctuated equilibrium does not support Darwin's original theory at all. Instead, it lines up more closely with a biblical view of instantaneous appearances of new species on earth, with God as their creator, creating each species according to its own kind (Genesis 6:20). God, in this scenario, is the magician invoked to account for this apparent instantaneous creation of each new species according to their kinds.
Miller spends the rest of chapter four dispelling the misuse of punctuated equilibrium by Johnson and others to cast doubt on Darwinian evolution. A key to his argument is the discussion of the phrase "geological instant." Miller notes that a "geological instant" is not really an instant. In the long course of the 4.5 billion year geological history of the earth, an "instant" is actually quite a long time, millions of years in fact. Miller points out that what Gould and Eldredge refer to as instantaneous speciation events actually cover millions of years of evolution. Gould and Eldredge were of course supporters of evolution. They simply demonstrated that, relatively speaking, evolution and the change of species actually happens quite quickly on the geological timescale and then species are stable for longer periods of time. Yet, they still evolved, they still shared common ancestors.
Miller's biggest problem with Johnson and others like him is not just that they are wrong in their understanding of evolution and science, but rather, the theological implications of their interpretations of the evidence. Namely, if Johnson is correct, and each new species is created instantaneously and magically by God, then what does that say about God. Specifically, since the fossil record demonstrates that most of the species that have ever lived on this planet have gone extinct, then God must not be a very good designer. He had to create each species magically, only to have most of them become extinct. What kind of a God creates like that? Miller asks.
Miller ends his chapter this way:
Intelligent design advocates have to account for patterns in the designer's work that clearly give the appearance of evolution. Is the designer being deceptive? Is there a reason why he can't get it right the first time? Is the designer, despite all his powers, a slow learner? He must be clever enough to design an African elephant, but apparently not so clever that he can do it the first time. Therefore we find the fossils of a couple dozen extinct almost-elephants over the last few million years. What are these failed experiments, and why does this master designer need to drive so many of his masterpieces to extinction? (p. 127).